U.S. patent application number 09/736619 was filed with the patent office on 2001-10-18 for tracking of clinical study samples, information and results.
Invention is credited to Markidan, Igor, Melnick, Jerald H., Oberoi, Himanshu.
Application Number | 20010032060 09/736619 |
Document ID | / |
Family ID | 22619828 |
Filed Date | 2001-10-18 |
United States Patent
Application |
20010032060 |
Kind Code |
A1 |
Markidan, Igor ; et
al. |
October 18, 2001 |
Tracking of clinical study samples, information and results
Abstract
A method for the tracking of biological samples and information
obtained from those samples during clinical studies is provided. In
particular, the present invention provides a method that
facilitates the tracking, analysis, and reporting of genotype
information derived from biological samples taken from individuals
during clinical studies. The method includes recording
predetermined characteristics of biological samples in a database,
determining procedures to be performed on those samples,
determining sample attributes to be recorded, preparing a checklist
that includes the procedures and attributes, storing the checklist
in the database, performing the procedures and recording the
results in the database. The present invention provides an
automated system for tracking clinical study protocols, and allows
access to information regarding a clinical study to be obtained
from a central database. Accordingly, reports regarding the
location, chain of custody, test results, and other information
concerning samples in a study can be obtained in a highly automated
fashion.
Inventors: |
Markidan, Igor; (Cherry
Hill, NJ) ; Oberoi, Himanshu; (Newton, MA) ;
Melnick, Jerald H.; (Wayland, MA) |
Correspondence
Address: |
SHERIDAN ROSS P.C.
Suite 1200
1560 Broadway
Denver
CO
80202-5141
US
|
Family ID: |
22619828 |
Appl. No.: |
09/736619 |
Filed: |
December 13, 2000 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60170432 |
Dec 13, 1999 |
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Current U.S.
Class: |
702/182 |
Current CPC
Class: |
G06Q 10/10 20130101 |
Class at
Publication: |
702/182 |
International
Class: |
G06F 011/30 |
Claims
What is claimed is:
1. A method for tracking samples of a clinical study, comprising:
defining a first clinical study protocol comprising a plurality of
procedures, wherein said procedures comprise steps; accessioning
samples for said first clinical study protocol by recording in a
database identifying information for said samples and
identification of said first clinical study; creating a worklist by
assigning a particular scientist to perform a particular procedure
on particular samples; creating a checklist comprising steps of at
least one procedure to be performed on the samples of a worklist;
performing said steps of said checklist; and recording in said
database completion and results of at least a portion of said steps
on said checklist.
2. The method of claim 1, further comprising conducting the steps
of said method with regard to a second clinical study protocol,
wherein said step of accessioning samples includes associating at
least a first sample with said first clinical study protocol and at
least a second sample with said second clinical study protocol, and
wherein at least one worklist assigned to a particular scientist
comprises at least one sample associated with said first clinical
study protocol and at least a second sample associated with said
second clinical study protocol.
3. The method of claim 1, wherein said step of indicating
completion and results of at least a portion of said steps on said
checklist comprises indicating completion of at least one step for
all samples on a checklist by one entry of information.
4. The method of claim 1, wherein at least one of said procedures
determines the genotype of an individual.
5. The method of claim 1, further comprising formalization of said
results by an activity selected from the group consisting of:
inspection of results; inspection of chain of custody records;
entry of new results; inspection of procedures run; and
modification and rejection of erroneous results.
6. A computer implemented method for tracking samples of a clinical
study, comprising the steps of: providing a computer having an
associated memory; providing a list of standard operating
procedures, wherein each of said standard operating procedures
comprise procedure steps; providing a list of samples; and merging
said list of standard operating procedures with said list of
samples to generate a check list for use in connection with said
clinical study, wherein said list of standard operating procedure,
said list of samples and said checklist are all stored in said
computer memory.
7. The method of claim 6, wherein at least one of said procedures
determines the genotype of an individual.
8. A computer implemented method for tracking samples of a clinical
study, comprising: providing a computer; accessioning a plurality
of samples, wherein identifying information is stored in said
computer; determining procedures to be taken with respect to said
samples, wherein said procedures comprise a plurality of steps;
defining at least a first workgroup comprising at least a first of
said plurality of samples, wherein said first workgroup comprises
at least one procedure, and wherein said workgroup is stored in
said computer; preparing at least one checklist comprising said at
least a first workgroup and said steps comprising said at least one
procedure, wherein said checklist is stored in said computer;
performing said steps; and recording performance of said steps in
said computer.
9. The method of claim 8, wherein at least one of said procedures
determines the genotype of an individual.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority under 35 U.S.C.
.sctn.119(e) from U.S. Provisional application Ser. No. 60/170,432,
filed Dec. 13, 1999, which is incorporated herein by reference in
its entirety.
FIELD OF THE INVENTION
[0002] The present invention relates to the tracking of samples and
information obtained from those samples during clinical studies. In
particular, the present invention relates to the tracking,
analysis, and reporting of genotype information derived from
biological samples taken from individuals participating in clinical
studies.
SUMMARY OF THE INVENTION
[0003] Management of information is an important aspect of
conducting clinical studies. However, traditional paper based
systems that have heretofore been used in such studies suffer from
a number of disadvantages. For example, accurate tracking of a
sample taken from an individual is difficult because it requires
the step that a scientist record on paper the identifier of the
sample and all related information produced as that sample
progresses through a study. Such a paper based system can result in
the loss of crucial information and makes difficult the retrieval
of subject attributes and other information concerning individual
samples. Auditing of samples from the clinical study and
establishing a chain of custody concerning samples is also
extremely difficult using paper based systems. In the context of
genotyping clinical laboratories, the problems and difficulties
associated with paper based tracking systems are magnified. In
order to be of use, information for an individual must include
genotype information for a desired gene recorded together with
medical information about the individual from which the DNA was
isolated. Such medical information typically includes age, sex,
ethnic background and medical parameters such as cardiovascular
statistics, blood pressure and blood analysis. At any one time,
hundreds and sometimes thousands of DNA samples can be collected
from individuals participating in a clinical study. Thus, accurate
tracking of genotype information in an easily retrievable form
during a clinical study is extremely complicated and cumbersome
when using a traditional paper based system.
[0004] The system of the present invention provides for the
automated tracking of clinical study protocols, and in particular
of genotype information obtained from a clinical study. The system
integrates the tracking of individual samples using bar code
identifiers and computerized scanners, with checklists of
procedures to be performed with respect to each of the samples by
scientists. Information regarding the status and location of
samples is stored in a central database, allowing for the
generation of complete location, chain of custody, test results and
other reports in a highly automated fashion. Additionally, the
system of the present invention provides for the auditing of
laboratory procedures used on samples from clinical studies.
Auditing in this context includes, but is not limited to, a
complete historical journal of all modifications and changes made
to data related to the sample and clinical study after initial
entry of sample information.
[0005] Additional advantages of the present invention will become
readily apparent from the following discussion, particularly when
taken together with the accompanying drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0006] FIG. 1 is a flow chart of the major process steps of the
present invention;
[0007] FIG. 2 is a screen shot of a study set up screen according
to an embodiment of the present invention;
[0008] FIG. 3 is a screen shot of an accessioning screen according
to an embodiment of the present invention;
[0009] FIG. 4 is a screen shot of a sample tracking screen
according to an embodiment of the present invention;
[0010] FIG. 5 is a screen shot of a sample worklist according to an
embodiment of the present invention;
[0011] FIG. 6 is a screen shot of an electronic laboratory
procedure checklist according to an embodiment of the present
invention;
[0012] FIG. 7 is a screen shot of a procedure dialogue according to
an embodiment of the present invention;
[0013] FIG. 8 is a screen shot of a procedure steps screen
according to an embodiment of the present invention;
[0014] FIG. 9 is a screen shot of a genotype results screen
according to an embodiment of the present invention;
[0015] FIG. 10 is a screen shot of an auditing screen according to
an embodiment of the present invention; and
[0016] FIG. 11 is a screen shot of a reporting screen according to
an embodiment of the present invention.
DESCRIPTION
[0017] In accordance with the present invention, a
computer-implemented method for tracking: (1) clinical study
samples through a clinical study; (2) the progress of a clinical
study; and (3) recording the results obtained from procedures
conducted during a clinical study is provided. Reference herein to
"tracking samples of clinical study" and similar terms can refer to
maintenance of the following information regarding samples in a
clinical study: patient information from the sample source;
physical location of samples; processing done to the sample; and
results of procedures done to the sample. The present method is
particularly useful for organizing and recording genotype
information from a clinical study and long-term management of
archives of samples derived from a clinical study. The present
invention is particularly useful for clinical studies that use
high-throughput activities that generate significant amounts of
complex data.
[0018] With reference to FIG. 1, the major steps comprising the
disclosed method are illustrated. The study is generally
initialized by defining the clinical study or protocol including
laboratory procedures to be followed. Once these initializing steps
have been taken, study samples may be received and accessioned.
Worklists assigning individual scientists to conduct specific
laboratory procedures on particular samples may be created after
the samples have been accessioned. Checklists comprising procedural
steps to be completed with respect to associated samples, and
generally grouping samples by common procedures found in worklists,
may then be created. The scientist then performs each procedural
step, and records progress through steps by recording their
completion on the checklist. After completion of the indicated
procedures for each sample, the scientist then records the results
obtained from each step. Following entry of the results, reports
may be generated in response to queries. Additional functions, not
illustrated in FIG. 1, include sample tracking, which allows the
location and condition of samples to be recorded at every stage of
the study, and auditing features that allow study directors to
confirm that proper procedures have been followed with respect to
the samples and monitor the accuracy of changes or corrections made
to data as it was initially entered.
[0019] Defining a laboratory procedure generally includes
describing the steps of the procedure that scientists may be
required to perform, and the equipment and products that may be
used in connection with the described procedure. In addition,
attributes of interest concerning individuals providing samples to
the study are identified. Laboratory procedures definition may, in
the context of a typical research laboratory, be conducted by
laboratory managers.
[0020] Study protocol definitions may generally include the
identification of the sponsor company, sponsor representative,
and/or clinical investigator associated with each study protocol.
The specific subject attributes to be tracked and/or the terms used
to describe those attributes are identified. During study protocol
definition, the particular laboratory procedures to be executed as
a part of the study are identified, as is the order in which the
procedures are to be performed. Additionally, the step of study
protocol definition includes defining the genotype information to
be reported. A typical screen allowing for entry of information
during the step of study protocol definition, according to one
embodiment of the present invention, is illustrated in FIG. 2.
[0021] Procedures are definitions which when constructed fully
describe the laboratory methods by which a sample must be processed
to fulfill a standard operating procedure (SOP) and generally
include one or more ordered steps. Where these procedures have been
formally approved, they may be referred to as standard operating
procedures (SOPs). As illustrated in FIG. 7, a procedure has an
identifying name and description. Procedures are also characterized
by any gene and/or allele that might be identified by the
procedure. Procedures may also include an indication of whether or
not the procedure has been formally approved and whether or not it
is obsolete.
[0022] Procedures are defined by their steps, which may be of
various types, such as simple laboratory process descriptions with
associated check boxes (for acknowledging a process completion,
e.g. centrifugation), text boxes (for entering additional
information on a process), sample transfers (for recording movement
of all or part of a sample from one tube or well of a plate into
another), reagent addition steps (for tracking addition of
reagents, e.g., oligonucleotides, enzymes or premade mixtures),
dilutions (for recording reduction of the concentration of a
sample), DNA concentration adjustments, and other sample
preparation steps, as illustrated in FIG. 8. According to the
system of the present invention, the steps comprising an individual
procedure are highly customizable and have provisions for automatic
creation and modification. Steps are defined by descriptions of the
action a user will need to perform. Steps are also characterized by
a "level" which is either individual or batch. If the level is
individual, the step must be performed on each sample individually.
If the level is batch, the step can be performed on the samples
either individually or as a set.
[0023] Referring now to FIG. 3, a computer screen according to one
embodiment of the present invention, associated with the step of
accessioning, is illustrated. Accessioning generally comprises
cataloging samples to be used as part of a study into the system.
Therefore, accessioning may include the scanning of bar codes
assigned to individual samples, associating the particular samples
with the study, and recording relevant attributes of the
individuals from whom the samples were obtained. Accordingly, the
system allows multiple sample tubes taken from the same or
different individuals to be registered. By providing for the
computerized registration of the samples, a number of benefits are
achieved. For example, the system provides validation checks for
accession and tube identifiers by ensuring uniqueness and
consistency of numeric codes and tube identifiers. In addition, the
system enforces the entry of the defined subject attributes of
interest. A computer screen for allowing the tracking of individual
sample tubes according to one embodiment of the present invention
is illustrated in FIG. 4.
[0024] Following the accession of samples, worklists can be
created. A computer screen illustrating a sample worklist according
to an embodiment of the present invention is illustrated in FIG. 5.
The worklist can assign individual samples to particular
scientists. This assignment may be performed by individual
scientists themselves, or by clinical study directors or other
clinical study management personnel. In general, a worklist
organizes samples according to a variety of relevant criteria
including but not limited to like procedures that are to be
performed on them. Thus, different samples requiring analysis using
the same procedure can be grouped together and assigned to the same
scientist to allow that scientist to process samples in batches,
thereby improving the efficiency of the laboratory. The system of
the present invention allows samples from multiple studies to be
assigned to an individual research scientist. Again, this allows
the efficiency of the laboratory to be increased by enabling
samples to be processed in batches, while ensuring that the
individual samples and data regarding those individual samples are
associated with each other and the correct study. As shown in FIG.
5, the worklist typically identifies the location of individual
samples, facilitates obtaining consent for use of the samples
before permitting procedures to be run on the samples and in so
doing ensures that an accurate and detailed chain of custody is
maintained.
[0025] Through the use of worklists, the system of present
invention facilitates the location and tracking of samples such
that large numbers of samples maybe accurately and efficiently
stored for long term periods in containers, refrigerators, and
freezers and later retrieved for additional analysis. These
capabilities as described are particularly useful for banking of
samples for additional or incremental reprocessing in retrospective
or prospective scientific or clinical studies.
[0026] A laboratory procedure checklist according to an embodiment
of the present invention is illustrated in FIG. 6. The checklist
describes how to perform a given procedure, and identifies samples
that are to be processed using that procedure. The checklist may
comprise a group of samples from a worklist, and the specific steps
of a given procedure that are to be performed on the samples. A
checklist is created by identifying the procedure to be conducted
and the samples to be used by, for example, scanning in a barcode
associated with a container of a given sample to be included in the
checklist. No modifications to the steps of a procedure may be
specified once a checklist derived from the procedure is populated
with one or more samples. Once a procedure has been used as a basis
for a checklist, the procedure can only be accessed for
viewing.
[0027] A checklist is executed by performing each step of a
specified procedure for each sample in the checklist. All of the
steps of a procedure must be completed sequentially on each sample
in the checklist. Thus, the first step of a procedure can be
conducted for all of the samples in a checklist, then the second
step can be conducted and so forth. Additionally, the checklist
provides specific methods defined by the procedure steps to track
the processing of samples. One such method is the use of check
boxes that require the scientist to check the step off as it is
completed, ensuring that the scientist keeps an accurate record of
the scientist's progress through the work flow. Complex processes
such as the movement of samples, and the separation or combination
of samples, are enforced, recorded and tracked using specialized
methods with configurable dialogue windows as defined by steps
within the checklist. Exchange of data to and from robotics
instrumentation may also be directed and managed from specialized
steps defined in the procedure checklist. To ensure that
identifying information is accurately recorded, and to provide at
least partially automated data entry, the samples may be
individually identified using a bar code, and that bar code read
using a scanner operatively connected to the system. After the
processing of an individual sample associated with a checklist is
complete, the scientist assigns it a status of "passed" or
"failed". Once all of the samples in a particular checklist have
been associated with a status, the checklist is assigned the status
of "completed" and can no longer be modified in any way.
[0028] The results of the procedures performed on samples are
recorded by the scientist in the checklist window and related
interfaces specific to the laboratory technologies employed. In
addition, the system of present invention includes an interface to
formalize the review of test results such that the results are
secured and accessible to the Study Director for the purpose of
inspection of results, inspection of chain of custody records,
entry of new results, inspection of procedures run and modification
or rejection of erroneous results. Final results for an individual
in a clinical study are declared final and correct by virtue of
completion of results review by the Study Director. Therefore, the
system of the present invention provides one integrated system that
allows for both the completion of procedural steps and production
of records containing the test results. The results of each
procedure may then be selectively grouped in response to queries
and reports generated. A window according to an embodiment of the
present invention illustrating sample genotype results is shown in
FIG. 9. When entering information indicating completion of
procedure steps which are identified as check box, textual or
factual steps, such information can be entered for all samples at
one time.
[0029] In a preferred embodiment, each of the above-described major
steps of the disclosed system are associated with a database that
serves as a central repository of the recorded information.
Therefore, at every stage of the clinical study, the status and
condition of individual samples and all of associated recorded
attributes may be accessed from the database. Additionally, the
status of procedures performed with respect to the samples may also
be accessed. Changes made to the database also are tracked by the
system, allowing complete and accurate auditing of samples from
clinical studies and associated clinical study protocols. An audit
report, according to one embodiment of the present invention, is
illustrated in FIG. 10. The information included in an automated
audit report may be selected by the user, depending on the
parameters of interest.
[0030] Reports containing results of a clinical study can be easily
generated using the disclosed system. An example report according
to an embodiment of the present invention is illustrated in FIG.
11. As shown in FIG. 11, reports may include a variety of
information. In general, the system generates reports by querying
the database in which the clinical study information is recorded,
and using the results of the query to populate a spreadsheet.
Report types provided for by the system include, but are not
limited to, genotype results, DNA integrity, purification results,
sample lists, and audit trails. In addition, the system includes
other query and search capabilities. The query feature provides for
the identification of specific subsets of samples, such as a subset
which includes samples from a given study which were received on a
certain date, associated with a given worklist, or stored in a
particular container. Using the search capability, scientists can
locate the boxes, racks, plates and gels that contain the samples
they intend to act on or for which they want more information.
[0031] According to one embodiment of the present invention, the
disclosed system operates on a client server type computer network.
The function of the system maybe provided using any programming
language, such as VISUAL BASIC.RTM. (Registered trademark of
Microsoft Corporation). The database may be any typical database
program, such as ORACLE.RTM. (Registered trademark of Oracle
Corporation), and the spreadsheet may be MICROSOFT.RTM. Excel
(Registered trademark of Microsoft Corporation).
[0032] From the foregoing description, a number of unique aspects
of the disclosed method are illustrated. The method tracks
information about clinical study protocols, the samples collected
in conjunction with those protocols, the procedures used to analyze
samples, and the results obtained from analysis of samples from a
clinical study. The method also helps laboratory personnel that
produce genotype information ensure that they adhere to study
requirements and good laboratory practices regulations and that
they manage and document their work in efficient and effective
manner. The method also allows for archiving and efficient
retrieval of samples and their related information.
[0033] While various embodiments of the present invention have been
described in detail, it is apparent that modifications and
adaptations of those embodiments will occur to those skilled in the
art. It is to be expressly understood, however, that such
modifications and adaptations are within the scope of the present
invention, as set forth in the following claims.
* * * * *